Running Applications on The Sheffield University HPC Clusters

Transcription

1 Running Applications on The Sheffield University HPC Clusters Deniz Savas dsavas.staff.sheffield.ac.uk June 2017

2 Topics 1. Software on an HPC system 2. Available Applications 3. Available Development Tools 4. Available Parallel Environments 5. How to access software using modules

3 Software on the HPC Systems For information on software check the link Ganglia Portland, GNU,Intel Redhat 64bit Scientific Linux Intel Hardware Sun Grid Engine OpenMPI, MVAPICH

4 Applications on Iceberg and sharc When you first log into iceberg or sharc you are connected to a head-node that provides the gateway to the cluster of worker nodes. Only a small subset of applications are provided on the headnodes as their main purpose is to allow access to the worker nodes. If you intend to perform interactive work, you should use the qsh or qrsh command to connect to one of the worker nodes. To submit batch jobs to the cluster you should use the qsub command. The next set of slides assume that you are already working on one of the worker nodes (qsh session). You are allowed multiple qsh sessions simultaneously. Alternatively once you are on a worker node you can type xterm& or Xterm or uterm to open multiple sessions on the same worker node running under the same job.

5 Applications on Iceberg Following are a few of the popular application and packages that are are available on iceberg and sharc: Ansys Abaqus Dyna Castep Fluent IDL Matlab Maple Mathematica R For full list of what is available on iceberg see the following link: For full list of what is available on sharc see the following link:

6 Developing Applications Compilers and Development Tools The following compilers are available on both iceberg and sharc: GNU Compilers INTEL Compilers PGI Compilers NAG Compilers For further information on compilers and development tools please see:

7 Licensing policy Where possible commercial software are purchased on floating-license terms. A separate license-server serves licenses to the HPC cluster and to users own linux/unix/pc/mac based desktops. Some software providers allow our users to install the applications directly on their own workstations in the university For further licensing information of some of the popular software check the following linkhttp://

8 Software Development Environment Compilers Currently the following Compilers are available on iceberg and sharc; PGI compilers Intel Compilers GNU compilers NAG Compilers NVIDIA CUDA Compilers As the software provided changes over time, it is always advisable to use the module avail command to see what is currently available. For many of the compilers we continue to provide the older versions as well as the recent one. The module avail command will indicate what versions are still available.

9 Software Development Environment Libraries Currently the following Software Libraries are available on sharc or iceberg; NAG, Flamegpu, armadillo, BLAS, Boost C++, CUDA, cudnn, fftw, GDAL, geos, various Intel Performance Enhancement Libraries, LAPACK, OpenSSL, SCOTCH As the software provided changes over time, it is always advisable to use the module avail command to see what is currently available.

10 Software Development Environment Parallel Runtime and Development Systems Currently the following parallel systems are available on sharc or iceberg; MVAPICH2 OpenMPI (gcc version) OpenMPI (Intel version) OPENMPI (pgi version) As the software provided changes over time, it is always advisable to use the module avail command to see what is currently available.

11 Accessing Applications and Development Tools on iceberg and sharc Modules Environment Modules are the mechanism by which most of the software is made available on iceberg and sharc. Modules are not available on the head nodes As well as applications, compilers and libraries are also made available only via the modules mechanism.

12 Using Modules Once you are on a worker node type module avail to see a list of all the available modules Having discovered what is available you can then use the module load module_name command to setup your software environment to use a particular software or compiler or library You may load as many modules as you need for your task If you wish to remove a module you can use the module unload module_name command to do so To see what modules you are using at a particular time use module list If you are curious as to what changes a particular module is making to your environment use the command module show module_name

13 Demonstration Using modules List modules Available Modules Load Module Compiling an Application The fish program

14 Useful Links Further Information on the module system; Applications on iceberg and sharc; Development Tools on iceberg and sharc; Parallel Environments on iceberg and sharc

15 Help HPC Hub For basic Unix enquries Goes to the discussion group Questions for the administration team